Machine learning to predict 8*8 matrix values using three independent matrices
In principle, you can use a fully connected neural network with reshaping for this kind of problem. The questions you should ask yourself are:


Baselines: What are the simplest algorithms to approach the problem? How good would a human be?
What do I know? Are there any properties of the 8x8 matrix that will always be true? For example, it seems as if the values from left to right strictly increase. Same for top to bottom. This can be used!
Are the outputs independent? (e.g. having the (1,1) entry of the matrix, do I know something about the $(i, j)$ entry of it?


Then, of course, there are more specific things I could imagine. If you were not clear about (2), you might have (wrongly) used softmax/tanh/sigmoid in the last layer. You might simply have too little training data for neural networks. Your neural network implementation might be broken.